Hi, I don't know the difference between the use of the 'marray' package and the use of the function 'rma'. I would like to calculate the expression from raw data and to normalize all the data afterward. Thanks for your help, Jamila

The marray* packages are for spotted cDNA arrays, and rma, which is part of the affy package is for Affymetrix oligonucleotide microarrays. Either package can be used for calculating normalized expression values, but only for a particular microarray type. Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> <gjam@daimi.au.dk> 02/21/04 3:14 AM >>> Hi, I don't know the difference between the use of the 'marray' package and the use of the function 'rma'. I would like to calculate the expression from raw data and to normalize all the data afterward. Thanks for your help, Jamila _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

'marray' is a package designed for spotted two color arrays. rma is a function in the 'affy' package which is designed for Affymetrix chips. If your data is affymetrix, then you need the CEL files and something along this line : setwd("/path/to/cel/files") # change working dir OR you can use the option filenames in ReadAffy() raw <- ReadAffy() out <- rma(raw) expressionValues <- exprs(out) write.table( expressionValues, file="out.txt", sep="\t", quote=FALSE) This will get you the expression values in a matrix format. Regards, Adai. On Sat, 21 Feb 2004 gjam@daimi.au.dk wrote: > Hi, > I don't know the difference between the use of the 'marray' package and the use > of the function 'rma'. I would like to calculate the expression from raw data > and to normalize all the data afterward. > Thanks for your help, > Jamila > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >